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Title: A novel genetic variant of grapevine leafroll-associated virus-3 (GLRaV-3) from Idaho grapevines

item THOMPSON, BRANDON - University Of Idaho
item DAHAN, JENNIFER - University Of Idaho
item Lee, Jungmin
item Martin, Robert
item KARASEV, ALEXANDER - University Of Idaho

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2018
Publication Date: 3/15/2019
Citation: Thompson, B.D., Dahan, J., Lee, J., Martin, R.R., Karasev, A.V. 2019. A novel genetic variant of grapevine leafroll-associated virus-3 (GLRaV-3) from Idaho grapevines. Plant Disease. 103:509-518.

Interpretive Summary: In this work from Idaho vineyards, a novel genetic variant of GLRaV-3 (grapevine leafroll associated virus-3) was identified, sequenced, and newly named GLRaV-3-ID45. Though Idaho’s winegrape industry is fairly young in comparison to the most prominent US growing regions of California, Washington, Oregon, and New York, grapevine viruses are a concern in all viticulture regions. Some of these viruses are detrimental to grapevine health, crop load ratio, fruit characteristics, and ultimately to wine quality, while others cause only minor issues. A new detection method was also developed to identify GLRaV-3-ID45 in leaf petiole samples. ID45 genetic sequence has recently been confirmed in California and Brazil as well.

Technical Abstract: Grapevine leafroll-associated virus-3 (GLRaV-3) is a major constraint on the profitable grapevine cultivation. The virus is efficiently transmitted by mealybugs and soft scale insects, or through vegetative propagation by cuttings, and is present worldwide, wherever grapevines are grown. GLRaV-3 exists as a complex of genetic variants currently classified in several phylogenetic groups which can differ from each other by as much as 30% in nucleotide sequence of the whole genome. In the course of the GLRaV-3 testing of wine grapes in southern Idaho, plants of two grapevine cultivars were found to harbor a novel genetic variant of GLRaV-3, named ID45, which exhibited =80% nucleotide sequence identity level to the known GLRaV-3 isolates in its most conserved HSP70h gene. The ID45 variant caused no foliar symptoms in ‘Cabernet Sauvignon’ in the fall, and was demonstrated to have poor reactivity to commercial virus-specific antibodies. The entire 18,478-nt genome sequence of the GLRaV-3-ID45 was determined using a combination of high throughput and conventional Sanger sequencing, and demonstrated to have typical organization for the genus Ampelovirus (family Closteroviridae), with only 70 to 77% identity level to the GLRaV-3 genomes from other established phylogroups. We concluded that ID45 represented a new phylogenetic group of GLRaV-3. Database search using ID45 nucleotide sequence as a query suggested that this novel ID45 variant is present in at least one other grape-growing state in the U.S., in California. An RT-PCR based test was developed to quickly distinguish ID45 from a predominant, phylogroup 1 GLRaV-3 strain in single and mixed infections.